After creating /etc/default/virtualbox to shut down any VMs still running during host shutdown, these error messages appear during shutdown if a VM has been started and shutdown before shutting down the host:

This use of /etc/default/virtualbox is not documented in the 3.2.12 User Manual which only mentions using the file during automated installations. The source of information was the comment before the shudown_vms function in /etc/rc.d/rc.virtualbox shown below. The full function is shown because of its possibly relevant comment, # don't create the ipcd directory with wrong permissions!

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Sorry, there is no guaranteed response time for non-paying customers. Note that there are a lot of other tickets open.

Re your problem: I cannot reproduce it. I've just tried it out, works fine here. The comment about wrong permissions for /tmp/.vbox-ipc-xyz is there because if that directory still does not exist, the script must not call VBoxManage, otherwise it would create this directory with the wrong permissions and the user would not be able to start his VM next time. The script also presumes that it is executed by root (which is normally the case because this script is executed during shutdown).